agentic-proteins 0.3.6

Deterministic protein design runtime with replayable execution artifacts, CLI automation, and API surfaces for lab-in-the-loop workflows

agentic-proteins

agentic-proteins provides the deterministic execution engine for protein design workflows, including replayable runtime artifacts, policy-safe runtime state transitions, CLI automation, and API boundaries.

Use this package when you need production execution behavior, traceable artifacts for auditability, or runtime integration points for agentic and lab-in-the-loop protein design systems.

Why teams pick this package

• reproducible execution with deterministic run state and replay-oriented controls
• inspectable artifacts for scientific review, incident analysis, and compliance
• integration-ready boundaries for CLI usage, API orchestration, and provider wiring
• clear runtime contracts that keep orchestration behavior stable across releases

Typical use cases

• run deterministic protein design loops in CI, batch systems, or orchestrators
• capture run artifacts as evidence for downstream review and approval workflows
• expose runtime capabilities through CLI or HTTP integration surfaces
• enforce provider capability checks before expensive or irreversible execution

Installation

pip install agentic-proteins

Quick start

agentic-proteins --help

Import-driven usage starts from the runtime and design loop modules:

from agentic_proteins.runtime import models as runtime_models
from agentic_proteins.design_loop import orchestrator

Package boundaries

This package owns runtime execution, lifecycle state, run artifacts, and runtime-facing entrypoints.

It does not own cross-package scientific governance:

• domain lifecycle and review-gate semantics live in bijux-proteomics-core
• ranking and scenario reasoning live in bijux-proteomics-intelligence
• evidence trust and contradiction resolution live in bijux-proteomics-knowledge
• lab scheduling and rerun planning live in bijux-proteomics-lab

Source guide

• src/agentic_proteins/runtime for runtime lifecycle and execution control
• src/agentic_proteins/design_loop for design-loop orchestration
• src/agentic_proteins/interfaces for CLI surfaces
• src/agentic_proteins/api for HTTP-facing boundaries
• tests for executable behavior expectations

Documentation

• Package guide
• Ownership boundary
• Architecture overview
• Interface contracts
• Release and versioning

Changelog

All notable changes for agentic-proteins are recorded here.

Unreleased

Changed

• No unreleased changes yet.

0.3.6 - 2026-04-20

Changed

• Prepared the v0.3.6 release line by aligning fallback versions and inter-package dependency floors across the repository.
• Synchronized release automation and governance with the bijux-std v0.1.3 shared standards baseline.

Fixed

• release-pypi.yml now uses parse-safe publication gating for token/bootstrap checks.
• Protected workflow policy checks now accept shared-manifest-driven standards updates through approved control paths.

0.3.5 - 2026-04-19

Changed

• Maintainer release documentation now references the split repository release workflows (release-artifacts.yml, release-pypi.yml, release-ghcr.yml, release-github.yml) instead of legacy publish workflow names.
• README docs badges and package metadata documentation links now point to the numbered handbook route 02-agentic-proteins for stable docs navigation.

0.3.4 - 2026-04-11

Changed

• Release history now records the synchronized v0.3.4 proteomics publication line used by the shared tag-driven release workflow.

0.3.3 - 2026-04-10

Changed

• Release history now records the synchronized v0.3.3 proteomics publication line used by the shared tag-driven release workflow.

0.3.2 - 2026-04-10

Changed

• Release history now records the synchronized v0.3.2 proteomics publication line used by the shared tag-driven release workflow.

0.3.1 - 2026-04-06

Added

• Package family PyPI and docs badges were added to README and maintainer package notes for cross-package discoverability.

Changed

• README content was rewritten with clearer package value proposition, usage scenarios, installation, quick-start guidance, and boundary definitions.
• Package description text was enhanced for stronger PyPI search relevance and package discovery.

0.3.0 - 2026-04-06

Added

• Package-local release manifest and maintainer-facing package docs: README.md, docs/ARCHITECTURE.md, docs/BOUNDARIES.md, docs/CONTRACTS.md, and docs/maintainer/pypi.md.
• Package-local changelog publishing path wired in package and root metadata.

Changed

• Package URLs now consistently reference bijux.io/bijux-proteomics and github.com/bijux/bijux-proteomics.

Fixed

• Test path resolution now uses explicit monorepo-root detection so e2e, regression, and governance tests stay stable with nested package manifests.

0.2.3 - 2026-01-16

Added

• Expanded provider test coverage for ColabFold, OpenProtein, and local ESMFold utilities.
• Runtime capability validation tests and candidate filter unit coverage.
• Stability marking test for module annotations.

Changed

• Hardened local ESMFold utility tests to exercise error and success branches.

Fixed

• Reliability checks and helper tests to keep coverage and gating stable.

0.2.2 - 2026-01-16

Added

• Release alignment for docs, gates, and CI structure.

Changed

• Consistent documentation build and validation wiring.

Fixed

• Minor release hygiene issues discovered in CI.

0.2.1 - 2026-01-16

Added

• Expanded unit and integration coverage with new invariants, API, and docs gates.
• Additional tests for provider isolation, reproducibility, and abuse-case blocking.
• Fancy PyPI readme fragments for README + changelog publishing.

Changed

• Refactored tests/unit into a structured layout for clearer ownership.

Fixed

• Coverage floors and CI gates stabilized around new test layout.

0.2.0 - 2026-01-16

Added

• Architecture invariants, threat model skeleton, and design debt ledger.
• Reproducible runs via agentic-proteins reproduce <run_id> with hash checks.
• Determinism tests, artifact immutability tests, and invariant regression coverage.
• Provider isolation checks and chaos failure test for mid-run provider loss.
• Benchmark regression gate and per-module coverage floors in CI.
• Documentation system contracts, lint gates, and CLI surface audit coverage.
• API error taxonomy enforcement, correlation ID logging test, and OpenAPI drift guard.
• Dependency allowlist enforcement for SBOM changes.

0.1.0 - 2026-01-14

Added

• Deterministic, artifact-first execution engine with explicit run directories and state snapshots.
• Agent-based architecture covering planning, analysis, execution, verification, and reporting.
• End-to-end design loop with failure handling, stagnation detection, and human-in-the-loop gating.
• CLI for running, resuming, inspecting, comparing, and exporting protein design runs.
• Local and remote provider abstractions with explicit capability and requirement checks.
• Structured reporting system with machine-readable artifacts and human-readable summaries.
• Integrated evaluation pipeline supporting structure-based metrics and ground-truth comparison.
• Reproducibility controls, observability hooks, and execution telemetry.
• Example datasets and reference runs for local experimentation and validation.
• Comprehensive test suite covering unit, integration, regression, and execution boundaries.